Author: Biqing Li
April 10, 2020
To access how many reads are sufficient for confidently call VDJ chain type. I subsampled 0.17, 0.33, 0.50, 0.67, 0.83 and 1 of the total VDJ reads from the VDJ demo data. Then I compared the performance from the following aspects
| BCR_reads | TCR_reads | mRNA_reads | BCR_reads_per_cell | TCR_reads_per_cell | mRNA_reads_per_cell | No. Cell | |
|---|---|---|---|---|---|---|---|
| 0.17 | 1820500 | 3122026 | 7795724 | 677.0 | 1161.0 | 2899.1 | 2689 |
| 0.33 | 3536562 | 6065149 | 7795724 | 1352.9 | 2320.3 | 2982.3 | 2614 |
| 0.50 | 5360966 | 9192825 | 7795724 | 2050.9 | 3516.8 | 2982.3 | 2614 |
| 0.67 | 7183869 | 12324310 | 7795724 | 2721.2 | 4668.3 | 2952.9 | 2640 |
| 0.83 | 8899642 | 15268995 | 7795724 | 3437.5 | 5897.6 | 3011.1 | 2589 |
| 1 | 10722634 | 18398174 | 7795724 | 4077.0 | 6995.5 | 2964.2 | 2630 |
| 0.17 | 0.33 | 0.50 | 0.67 | 0.83 | 1 | |
|---|---|---|---|---|---|---|
| Reads_Cellular_Aligned_to_VDJ | 3990815.00 | 7751682.00 | 11748252.00 | 15747435.00 | 19511039.00 | 23508003.00 |
| Reads_CDR3_Valid_Unfiltered | 3135000.00 | 6089575.00 | 9229733.00 | 12372514.00 | 15330701.00 | 18472896.00 |
| Reads_CDR3_Valid_Putative | 2799438.00 | 5279049.00 | 8035262.00 | 10882897.00 | 13208413.00 | 16154927.00 |
| Pct_Reads_CDR3_Valid_from_Putative_Cells | 89.30 | 86.69 | 87.06 | 87.96 | 86.16 | 87.45 |
| Reads_CDR3_Valid_Putative_Corrected | 2605679.00 | 4910067.00 | 7475808.00 | 10151168.00 | 12334222.00 | 15074284.00 |
| Pct_Reads_CDR3_Valid_Corrected_from_Putative_Cells | 83.12 | 80.63 | 81.00 | 82.05 | 80.45 | 81.60 |
| Mean_Reads_CDR3_Valid_Corrected_per_Putative_Cell | 969.01 | 1878.37 | 2859.91 | 3845.14 | 4764.09 | 5731.67 |
| Molecules_Unfiltered | 86790.00 | 120888.00 | 152504.00 | 182416.00 | 209337.00 | 237544.00 |
| Molecules_Corrected_Putative | 40017.00 | 43808.00 | 47067.00 | 50209.00 | 51506.00 | 53779.00 |
| Mean_Molecules_Corrected_per_Putative_Cell | 14.88 | 16.76 | 18.01 | 19.02 | 19.89 | 20.45 |
| 0.17 | 0.33 | 0.50 | 0.67 | 0.83 | 1 | |
|---|---|---|---|---|---|---|
| BCR_Heavy | 9651 | 10656 | 11413 | 12305 | 12784 | 13250 |
| BCR_Kappa | 8703 | 9622 | 10212 | 10574 | 10867 | 11133 |
| BCR_Lambda | 5999 | 6487 | 6844 | 7044 | 7225 | 7381 |
| TCR_Alpha | 5877 | 6276 | 6893 | 7537 | 7656 | 8230 |
| TCR_Beta | 7989 | 8724 | 9464 | 10353 | 10472 | 11145 |
| TCR_Delta | 591 | 652 | 746 | 788 | 825 | 862 |
| TCR_Gamma | 1207 | 1391 | 1495 | 1608 | 1677 | 1778 |
| 0.17 | 0.33 | 0.50 | 0.67 | 0.83 | 1 | |
|---|---|---|---|---|---|---|
| T_CD4_memory | 451 | 409 | 427 | 447 | 424 | 445 |
| T_CD4_naive | 273 | 264 | 269 | 283 | 270 | 280 |
| T_CD8_memory | 171 | 167 | 167 | 171 | 167 | 169 |
| T_CD8_naive | 95 | 92 | 92 | 96 | 94 | 96 |
| T_gamma_delta | 52 | 51 | 55 | 52 | 54 | 54 |
| B | 232 | 238 | 239 | 240 | 241 | 242 |
The cell with any void V/D/J segment will be removed
The cell with any void V/D/J segment will be removed
Thank you!